Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale

Abstract

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R(2) = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

FIG. 1.

(A) Rarefaction results for soils with low (PE5), average (MT2), and high (CC1) levels of diversity. The same three soils were also used for Fig. 3. (B) Rarefaction results for the five dominant bacterial phyla across all soils combined. To make the patterns clear, we have shown rarefaction curves for only the first 20,000 sequences per group. PE5, Manu National Park, Peru, tropical forest soil, pH 3.6; MT2, Missoula, MT, temperate coniferous forest, pH 6.7; CC1, Cedar Creek LTER, United States, temperate grassland, pH 6.0.

FIG. 2.

Relative abundances of dominant bacterial taxa in all soils combined and in soils with different pH levels. The numbers above the columns indicate the number of soils included in each category. Relative abundances were estimated from the proportional abundances of classifiable sequences, excluding those sequences that could not be classified below the domain level. For additional taxonomic descriptions of the soil bacterial communities, see Tables S1A and S1B in the supplemental material.

FIG. 3.

Relationship between soil pH and soil bacterial diversity, measuring using Faith's PD (A) and the number of phylotypes (B), with phylotypes defined at the 97% sequence similarity level. Lines represent the best-fit quadratic model to the data. Unfilled triangles represent the three soils shown in Fig. 1A. Diversity indices were calculated using 1,200 sequences per soil sample.

FIG. 4.

Nonmetric multidimensional scaling plots derived from pairwise Unifrac distances between soils, with symbols coded by general ecosystem type (A) and pH category (B).

FIG. 5.

Correlations between relative abundances of the five dominant bacterial phyla and soil pH. Pearson correlation coefficients (r) are shown for each taxon, with the associated Bonferroni-corrected P values.